Stargate: Ancient Reincarnation Episode 1
by Spearhead
Summary: A continuation of Stargate: Atlantis. Set after Season 5. After Enemy at the Gate.   The SGC has been shutdown and all operations have been moved to the cloaked city of Atlantis. As the universe slips into chaos, a new hope arises.
1. Chapter 1

Stargate: Ancient Reincarnation.

Chapter 1

"I regret it's come to this, Colonel. To be honest, I've always admired you…but now you've gone too far." Woolsey said looking at the Colonel through the bars that made up Atlantis's shielded cell. Sheppard was sat on the bed that had recently been added to the cell along with a table and a stool.

"Maybe I should have gone further." John said sarcastically. The cell was just as it had always been, except for the recently Earth added comforts. Woolsey leaned closer to the bars.

"If there was any way to make this more pleasant for you, I would do it. But attempted to steal Atlantis was just too much." Woolsey explained.

"I did the right thing. I'm just sorry I didn't finish the job." John countered.

"General O'Neill is gathering a panel of your peers. It shouldn't take long." Woolsey sniffed.

* * *

><p>"Donnor, Davis, watch the gate," Colonel Morris ordered out a few minutes after his team arrived on the previously unexplored world through the Stargate. This was his teams second deployment in three days to this new world. This time, he bought back an archaeology team to explore the ruins.<p>

"Stevenson, you and me are on patrol. Take the southern ruins that we didn't get to last time. I'll show the archaeologist the empty rooms we found last time. Report anything interesting." Morris ordered.

"Yes sir." Stevenson smiled. The Captain turned south and walked off into the crumbling remains of an Ancient city. Though mostly made up of empty buildings and crumbling walls. A few, small pieces of ancient tech had been discovered on their first trip through the gate.

Nothing groundbreaking had been found, but the fact that some tech remained suggested that the planet hadn't been scavenged by the Goa'uld or others and that meant there might still be something worthwhile lying around.

Captain Ryan Stevenson had recently been reassigned by General Laundry at his request. SG-7, his previous team, wasn't tasked with exploring the remainder of the Gate Network. SG-14 on the other hand, were. So for that reason, it was a desirable post. Laundry had, at first, denied the transfer request. But after more than an hours debate, he'd agreed after Dr. Lam had signed off on his Medical 'permission' slip.

After half an hour of wondering through the ruins finding nothing than rubble, Stevenson checked in on his radio and headed to head back to the main structure where the Stargate was located. This was one of the few worlds that the Humans had explored that had the gate side of a structure. Which suggested to the experts back in the SGC that the planet might hold a greater significance than other Ancient sites they'd found.

There was even rumours floating around the SGC about establishing a permanent base in the ruins. While some of the buildings seemed intact to Stevenson, they weren't what he'd call liveable. Most had holes of some sort in them, and the local flora had grown up and through some of the buildings. This made it seem although the forest was warring with the city for dominance.

But that didn't really matter to him. He and his team would be moving on to the next address on the diminishing unexplored list within a few days. He hoped they'd be able to finish off the uncharted gates in the Milky Way before he was deemed unfit for duty. But they were calculating new addresses every day, so it looked unlikely.

Stevenson wound his way through the western edge of the ruins that he'd spied from afar earlier. There were several statues and large columns that seemed slightly out of place from the rest of the structures. Some of the large columns had even fallen over while all of the statues in the area looked brand new, except for the vines growing up their bases. They were clearly Ancient in design, but their coloration and placement suggested they weren't part of the original architecture.

As he walked down a wide corridor and past the foot of one large female statue Stevenson aimed his P-90 up in response to movement on his flank. He lowered the weapon when he recognized the source. A section of the pedestal had extended out towards him.

A memory from his initial SGC training clicked and he reached for his radio. General O'Neill had encountered this technology twice during his tour on SG-1. Stevenson's finger froze over the radio's call button as another thought struck him. He felt a flicker desperation shoot through his body but after a second, his mind dismissed the idea as ludicrous. He remembered that O'Neill had nearly died both times.

Without thinking his hand retreated from his radio. He looked down at it in wonder, realizing his instincts were disagreeing with his logic. Stevenson looked up at the partially deployed Ancient Repository of Knowledge and swallowed hard.

"I'm dead anyway, a million to one is better than no odds at all." He said to himself.

Stevenson pulled the green cap off his head and closed his eyes. He sucked in one last breath and stepped forward.


	2. Chapter 2

Review answers 

Starrystars'Unlocked: Don't worry, this isn't completely copied. The first few eps will be similar with slight differences, but this will be a AU. Also, I do have permission from Aer'Ki Jyr.

StargateFFWriter: You are right, changes will begin appearing I promise.

Thunder18: Glad you enjoyed it

Seshikago: Yes, yes I did.

Douchiesnackes: It does, doesn't it….have faith in me.

Chapter 2

"You've really done it this time, Colonel." Landry said from outside of Atlantis brig.

"Done what, exactly?" Sheppard asked sarcastically.

"Done what? Well, let's start with the obvious. Attempting to steal from the I.O.A. and SGC." Landry replied.

"Atlantis doesn't belong to Earth of the SGC. It belongs in Pegasus." Sheppard argued.

"Even if that's true, I was referring to the weapons and supplies you've been stockpiling for your return to Pegasus." Landry said smugly.

"How did you know?" John asked confused.

"I'll give Woolsey credit, he knows how to keep a track on supplies." Landry admitted.

"I should have known." Sheppard nodded from within his cell.

"Then, there's trying to steal Atlantis. We bought it back from Pegasus, we've lost lives defending it and we are damn well going to reek the benefits." Landry argued.

"So we just turn tail and run because the Wraith are proving more resilient than the Goa'uld did?" Sheppard argued loudly. Landry seemed to agree, but didn't say anything.

"The purpose of the Atlantis Expedition was to recover Ancient technologies from Pegasus and return them to Earth. It was to find technology capable of defending Earth from any threat. It was not, however, a mission to fight the Ancients war with the Wraith. The I.O.A. feels that even with the allies you've made in Pegasus, it still doesn't justify returning Atlantis or continuing the fight on their behalf. And trying to hijack the city for that purpose, was obviously futile." Landry explained looking Sheppard directly in the eye.

"We have allies to protect! They need our help! The Wraith will eventually come after us!" Sheppard shouted in objection.

"The I.O.A. doesn't agree with you. Pegasus was fine before we arrived, Pegasus will be fine without us. Who knows, maybe the Wraith will go back into hibernation." Landry replied.

"What happens if they should show up?" Sheppard inquired.

"Not that it's be any of you business, but with Atlantis fully powered, I've been reassured that we'll be able to take on the whole Wraith armada." Landry answered.

"So let me get this straight, I'm being punished for doing the honourable thing?" Sheppard questioned.

"When it was against standing orders, then yes. The I.O.A. has had it with your independent streak." Landry replied.

"Since when does the I.O.A. tell the US Air Force what to do?" John asked.

"They don't, but the President happens to agree with them and so do I." Hank answered.

"So what does this mean for me?" Sheppard asked the General.

"Most likely, life imprisonment. Or retirement off world. Your choice." Landry informed him.

"The second option sounds nice." Sheppard admitted.

"Don't think it will. The off world retirement doesn't include returning to Pegasus." Landry blocked Sheppard and his train of thought.

"Fine, but can't we arrange the evacuation of the human population from Pegasus?" Sheppard suggested.

"There at least I can sympathize. While I don't expect that we could evacuate an entire galaxy, we could at least provide refuge for some of the Humans allies. I don't like turning our backs on our allies any more than you do, Colonel, but the I.O.A. is ultimately the one in charge. And like it or not, we have to follow orders." Landry replied after a minute of thought.

"Even if they're bad orders?" John asked.

"Even if they're bad ones, Colonel. You've had too much leniency in Pegasus for your own good. Being a galaxy away from command influence probably didn't help matters any. I'll be sure to bring that point up at your court-martial," Landry said as he turned to leave.

"That's it? You just popped in to chat?" Sheppard asked.

"Believe it or not, Colonel, I have another soldier to discipline. Although I doubt he'll live out the month. He's probably better off, given the circumstances." Hank admitted.

"What happened? Did Ronan do something?" Sheppard asked.

"No, Colonel. He's one of mine. Seems he found an Ancient Repository and decided to use it on himself." Landry explained.

"What's an Ancient Repository?" John asked somewhat confused.

"General O'Neill refers to it as a 'head sucker'. Thing is it nearly killed him…twice. The Asgard saved his life both times, but Captain Stevenson won't have that luxury." Landry looked genuinely disappointed.

"Did he know it'd kill him?" Sheppard asked.

"Probably, only he knows for sure, and right now he's in a coma in the infirmary. Seems he disobeyed orders and didn't report it in. His team leader found him unconscious beneath the device."" Landry offered.

"How do you know he did it on purpose?" Sheppard asked.

"Standing up for another rogue, how touching." Landry said sarcastically.

"We found his hat several meters away from the device, along with some very distinctive footprints. He didn't just walk by and it grabbed him. Apparently he took his hat off before walking straight up to it and sticking his head in. Either way I'll find out for sure when he wakes up. I've got Dr. Jackson standing by to translate." Landry explained.

"Translate?" Sheppard asked, confused.

"Seems the Repository rewrites your brain with Ancient knowledge. General O'Neill eventually lost the ability to speak English." Landry approached the rooms door and it opened to reveal two Airmen guarding the room.

"If I were you I'd start planning your defence. Your designated council will be here in the next hour, but you're going to need as much prep time as you can get. If I weren't ticked with you I'd wish you luck, even though I know it wouldn't do you any good. You're going to be staring at the inside of a cell for most, if not all of your remaining life. That's if they don't grant you off world retirement." Landry guessed.

Landry exited the room and the door closed itself behind him, leaving Sheppard sitting alone behind in the sparse cell.

"Do we get any bathroom breaks? There's no toilet in here!" Sheppard shouted trying to gain someone's attention as there was no one in the area surrounding the cell.


	3. Chapter 3

Chapter 3

"Has he said anything?" Dr. Lam asked Daniel when she returned to Stevenson's bed after taking a brief lunch. The Atlantis Mess Hall was a lot more colourful than the old SGC cafeteria. Ever since Atlantis's return to Earth, the SGC had effectively moved into Atlantis. Departments from the SGC and Atlantis melded together which at first caused clashes, but now the whole city was enjoying a huge influx of resources, man power and funding.

"He woke up for about thirty seconds, complained about a headache, and passed out again." Daniel answered.

"In English?" she asked.

"Yes, why would he do this knowing that it was going to kill him?" He answered, then shook his head in disbelief.

"You don't know?" Lam looked at him puzzled.

"Know what?" Daniel stared at her. After over ten years at the SGC, he could tell when someone was hiding something.

"I'm not exactly supposed to reveal personal information, but I guess it won't hurt in this case. You probably need to know anyway if you're going to be talking to him. He has a degenerative genetic disease. He's not expected to live more than three more years." Caroline explained.

"I didn't know that." Daniel turned back and looked at Ryan.

"He wanted it kept a secret, and I was ethically forced to oblige as long as his illness didn't disqualify him from duty." Doctor Lam looked a little uncomfortable.

"How could it not?" Daniel asked.

"As long as he can handle the pain and carry out his daily tasks there's no medical reason to take him off the active duty list. His disease moves slowly, it's not like it's going to develop to a critical level during a mission. He'll slowly be subjected to more and more pain until he can't take it any longer or his superiors notice a physical inability. He said he didn't want them to know so that they wouldn't pull him off duty without a reason." Lam shrugged.

"I grudgingly agreed and have waited for a medical incident to indicate he was no longer fit for duty, but so far that hasn't happened. Either his condition isn't progressing as fast as predicted or he's hiding the pain well. Either way it's a moot point. The Ancient device is going to kill him long before his disease will." Lam said looking at Ryan.

"I guess he figured he didn't have anything to lose. Maybe he'll be able to tell us something useful and make his death worth something." Daniel sighed.

"He made it clear to me he didn't want to die helpless in bed, slowly withering away, at least this will be quick by comparison." Lam confided.

Suddenly the status monitors started wailing and Stevenson's body began to convulse. Lam reacted instantly and ordered up a cocktail of drugs.

"Did this happen to O'Neill?" Lam asked as took action.

"No, His physical deterioration happened after his mental conversion." Daniel said confused.

"This isn't good, his blood pressure is spiking, and his neural patterns are erratic. I don't know how long his body can take this…" Lam said alarmed. The constant tone of heart failure sounded as Stevenson's body fell still.

"Get the crash cart over here, now!" Lam yelled. Daniel watched dejectedly as Dr. Lam worked feverishly to revive the Captain, but she didn't have an effect. Ten minutes later Lam finally gave up and deactivated the medical equipment. She morosely pulled the bed sheet up over his head and hobbled away from the dead patient.

"There was nothing you could have done," Daniel said, trying to comfort her.

"I know," Lam said, not happy in the slightest.

"We knew this would happen, we just didn't think it would be this fast." Daniel admitted.

"A patient died in my infirmary, I don't like that." she said icily. Daniel put a hand on her shoulder supportively. He knew there wasn't anything that he could say to make it right. Losing people was always hard.

"You really blew it this time, Sheppard," O'Neill said as he paced back and forth in front of the cell.

"With respect, sir, as much as I could use a pep talk, what I really need is an ally who can do something about these charges." Sheppard said exasperated. The more days that passed the more he was beginning to lose his patience…and his already limited respect for authority.

"I can't get you out of this one, Sheppard. Both the President and the I.O.A. want your head. If you'd just defied the I.O.A.'s orders then maybe I could have done something, but stealing from the Air Force ticked the Commander in Chief off royally. They're going to eat you alive in the hearing tomorrow, then shuttle you off for the official beheading," O'Neill said metaphorically.

"Just, tell me. Why'd you have to go and do it?" Jack asked.

"Because it was the right thing to do. And I'd expect you of all people to understand that, General." Sheppard said with a bit of venom in his voice. He felt like he was being betrayed by everyone he'd ever remotely respected back on Earth. He seriously wished he'd gone through with the 'Steal Atlantis' plan. But at the last minute, his doubts got the best of him. He realised that even if he managed to fly Atlantis all the way back to Pegasus, there was no guarantee that the I.O.A. would leave the city there or that he'd manage to reach the Stargate without being arrested.

"What good did it do? You've been found out and your operations stopped. Are the people of Pegasus any better off than before? The Wraith are still there and nothing you did was going to stop that. You threw your career away for nothing." Jack just couldn't grasp Johns reasoning.

"At least I'll have a clear conscious when I go to sleep at night. I'll know that I did everything I could to save those people." Sheppard said determinately.

"Can you say the same, General?" John asked.

"Actually, I can, I fought the I.O.A. on this one, Sheppard and I fought hard. In the end it didn't change anything. Too many people see the logic in bringing back the technology we've found and destroying the Wraith's one and only route into our galaxy. They don't care about some faceless people they've never met nor ever will meet millions of light-years away…and there's nothing I can say or do that's going to change their mind." O'Neill countered half-heartedly.

"But you're okay with that fact that you're the one that's effectively giving millions of people the death sentence! " Sheppard reminded him. O'Neill thought about saying something, then stopped and swallowed instead.

"The I.O.A. is doing this, not us. I tried to get Atlantis back to Pegasus, but the President agrees with the I.O.A." Jack responded.

"And that's okay with you?" Sheppard asked.

"As a matter of fact, no it's not, but we can't go against the President." Jack answered.

"Whatever happened to disobeying orders when it was the right thing to do?" John asked again.

"Ah yes, the right thing to do." O'Neill said slowly, remembering back.

"I know you've been in this position before, General, and that you did the same thing as me." John said through the bars.

"But you got caught, Sheppard! More importantly, I didn't try to steal a flying city." O'Neill said, half joking, half sarcastic.

"If you're going to pull a fast one you've gotta be able to get away with it. Did you really think Woolsey wouldn't notice?" Jack asked.

"I didn't think about that, I was too busy worrying about people getting life-sucked by the Wraith to worry about the sleeping monsters among our own people." Sheppard admitted.

"I sympathize, Colonel. I really do. If it was up to me you'd be out bagging more bad guys, but the big wigs have stepped in and taken it out of my hands. And despite my best efforts to convince them to preserve Atlantis, they've decided that the remaining power in our ZPMs is too precious a commodity to waste flying the entire city back to Pegasus. I'll do what I can for you at the hearing, maybe get them to go easy on the confinement request, but it doesn't look good." O'Neill sighed.

O'Neill started to say something more into the silence, but thought twice about it. Neither he nor Sheppard had anything more to say so he finally, awkwardly got up to leave.

"Why is it that we shoot the bad guys on other planets, but here on Earth they get a free pass?" Sheppard asked.

"Job security." O'Neill said deadpan as he left. The automatic bulkhead closed behind the Head of Home World Command.


	4. Chapter 4

Chapter 4

The Atlantis sickbay was blissfully quiet and unoccupied while Dr. Lam wrote up the death certificate for Captain Stevenson on her computer. Dr. Jenifer Keller was on some much needed vacation time, so Caroline had taken over for the time being. Suddenly one of the nurses screamed in shock.

"What is it?" Lam yelled as she darted out of her seat and around the corner…where she saw Stevenson's body convulsing again.

"What the hell?" she said as she reactivated the medical sensors.

"Call the General and Mr Woolsey," Lam ordered as she held down Stevenson's arm so it wouldn't knock the meds off the nearby tray.

"Tell them it's an emergency." Lam barked.

Ten minutes later General Landry and Mr. Woolsey walked into the infirmary in stunned disbelief.

"You said he was dead?" Hank blurts out.

"He was, for four hours. Then he just came back…I can't explain it. His vitals are stabilizing, albeit slowly. He's gone through three convulsions in the past ten minutes and each time he comes out of it a little better off than before." Lam insisted

"Explain," Landry demanded.

"I can't," Lam said simply.

"Will he recover?" the General asked.

"If I had to guess, I'd say yes, but I'm really not qualified to give you an answer on this one. I have no idea what's happening to him, but he seems to me to be improving…despite being dead earlier." Caroline persisted.

"Well this complicates things." Landry sighed.

"How so?" Lam asked.

"_If_ he lives, what do you think the I.O.A. is going to say about it?" Landry said, stressing the 'if'.

"I don't catch your meaning." Lam said confused.

"If the Captain has the knowledge of the Ancients and lives to keep it…" Woolsey began.

"…they'll want to turn him into their personal oracle," she finished.

"Hmmn, 'oracle' is a bit more pleasant than what I was thinking about." Woolsey added.

Lam stared at him in disbelief. She'd never seen Richard Woolsey look so concerned before. Maybe that's what command did to someone.

"He's still an Air Force officer. They can't just treat him as a piece of property." Caroline offered.

"I agree, but that doesn't mean they won't try. I'll have to discuss this with General O'Neill before he leaves. Maybe we can head this one off early…and there's still the matter of how this happened in the first place." Hank planned.

"You don't think it was an accident?" Lam asked.

"I'm guessing he did it on purpose, but anything's possible. Let me know when he's lucid…or if things take a turn for the worse." Landry nodded before leaving with Woolsey close behind him.

Stevenson lay comatose in his bed, his body motionless aside from the occasional tremor. Daniel and Lam stayed with him as much as they could, waiting for a glimpse of consciousness. Days passed by with no external developments. On the inside, however, was an entirely different story.

His mind was hyper-processing a virtual reality simulation pre-programmed into the Ancient coding that had begun to rewrite his body and mind. He as living out days in a matter of minutes, facing challenge after challenge in a gruelling simulation designed to test his worth.

If he failed the test he would never remember having undergone it. He would wake up with the Repository of Ancient Knowledge in his mind, but the additional data cache hidden within the confines of the Repository would self-delete in one final security measure designed to insure that the Ancients' final hope wouldn't be discovered and destroyed before it could take effect.

This, however, was not to take place. Inside the virtual testing chamber Stevenson proved his worth and accepted the mandate given to him by proxy. He knew full well the significance of what he was getting himself into, the Ancients had made sure to give him every chance to decline the burden that was about to be placed on his shoulders.

He woke on the end of a deep breath, blinked his eyes and looked around.

"You're in the infirmary, Captain, you've been unconscious for over a week. Don't try to move just yet." Lam said from beside him.

"Can you understand us?" Daniel asked from the other side of the bed.

"_Yes, Dr. Jackson. My marbles are still in my head_," Stevenson said in Ancient.

Lam and Daniel exchanged glances.

"It seems a few of them have become a bit scrambled," Daniel explained to Stevenson.

"_How so_?" he asked a little confused.

"You're speaking in Ancient," Daniel said, making mouthing motions with his hand.

"_Am I? I hadn't noticed_. _I can understand you perfectly, but I can't for the life of me speak English_." He worked his mouth around, thinking about something, then a frustrated expression manifested itself on his blank features.

"Yeah well, we've seen this before with O'Neill. The Ancient Repository seems to overwrite your existing language patterns with its own. Eventually you may not even be able to understand English. In which case I'll be here to translate, so you're not completely cut off from society." Daniel reassured.

"_I don't think that's going to happen to me, but thanks just the same. Talk to you later_." Ryan said looking as if his strength was fading quickly.

"Later? You have somewhere to be?" Daniel asked sarcastically just as Stevenson's eyes rolled up into his lids and he started to convulse again.

"According to Dr. Lam, Captain Stevenson's body is also changing as a result of his contact with the Ancient device, from all indications his physiology is altering into a form similar to what we saw from the Anubis creation called Khalek. We squandered a unique opportunity for study then…we're not going to waste another opportunity now." William Parson said from across Atlantis's briefing room table.

"So what does the I.O.A. suggest? Confine him to a research lab for the rest of his life? This man is one of our own. He has rights." Landry asked irreverently.

"Don't think that we in the I.O.A. haven't considered that angle, but each and every one of our Stargate personnel know and accept the risks involved with exploring the galaxy. Captain Stevenson has essentially been hijacked by alien programming intent on remaking him into an alien. He's not Human anymore, or at least he won't be for very long." William explained.

"That's your argument? That'll never fly. He's still part of the U.S. military and he's not going anywhere unless I order him to." Landry asked, half laughing.

"That decision may ultimately not be up to us, or the President." Woolsey admitted.

"Never the less, I'm sure some arrangement can be reached to have him examined here in Atlantis. I'm sure your people are as anxious as we are to get access to the Ancient library within his mind. It's a freak of nature that he's survived to this point, and with any luck he'll hold on permanently…but if he doesn't and we've only got a limited amount of time for study, isn't it irresponsible to waste an opportunity such as this while we bicker back and forth about it here and up through the chain of command?" Parson suggested.

"Yes, there has been a bit of bickering involved, I've got Jackson with him now. If he has anything important to say we'll know about it immediately. We've also got a video feed on him 24/7." O'Neill said as he walked into the conference room.

"And I've got the biomed sensor that we took from Anubis's lab hooked up and monitoring him as we speak, not to mention Atlantis's internal sensors. Rest assured, we're not missing anything from a medical standpoint." Lam added.

"I'm pleased to hear that, It'll give us time to discuss any long-term research projects. In the mean time you will be forwarding any data gleamed from him to my quarters." Parson informed.

"Of course." Landry said, standing up. Parson nodded to both Generals then left the conference table, briefcase in hand and posse in tow.


	5. Chapter 5

Chapter 5

"_Where am I_?" Stevenson asked after waking up from another blackout, still speaking in Ancient.

"They've moved you into isolation." Daniel said from his side.

"_Why_?" Stevenson asked, puzzled.

"A little something to do with the fact that you admitted to intentionally sticking your head in the head sucker." Daniel explained.

"_Neural Interface_," Stevenson corrected.

"Right, well it seems you and all exploratory teams were given specific instructions in your indoctrination not to mess with an Ancient Repository if you ever ran across one," Daniel reminded him. Ryan nodded as he remembered.

"So why did you do it?" Dr. Jackson asked.

"_Certain death isn't very appealing_." he said sarcastically, though Daniel didn't pick up on that intricacy. His knowledge of the Ancient language was tolerable, but Stevenson was speaking it as if he'd done so his entire life.

"You mean you'd rather take a chance on a long shot instead of waiting around to die from a genetic disease?" Daniel asked.

"_You know about that_?" Stevenson seemed to become slightly distressed.

"They only told me after they brought me in to translate. No one else knows. Actually it's really a moot point now. Dr. Lam says the physical alterations taking place inside you are changing your DNA and have wiped out your disease in the process. It seems your long shot paid off…if you survive the transformation process." Daniel explained the good news.

"_Good. I was wondering about that. You can tell Lam that I'm past the worst of it. Each time I black out I'm experiencing an upgrade that requires my body and mind to shut down temporarily_." Stevenson informed.

"You know that for a fact, or just guessing?" Daniel queried raising an eyebrow.

"_I know_." Stevenson replied firmly.

"Really…what else do you know?" Daniel asked surprised.

"_What do you mean_?" Stevenson asked.

"Come on, you've got the entire Ancient library stored in your mind. Do you have access to any of the good stuff yet?" Daniel probed.

"_Like what_?" Ryan asked.

"What about Ancient history? Can you tell me anything new?" Daniel asked. Stevenson started to say something then stopped short.

"_Maybe later, Dr. Jackson. I'm still fighting a monster migraine and it requires something of a conscious effort to hold it in check_." Ryan replied as he leaned his head back onto the pillow and closed his eyes.

"Alright, I'll be back to check on you later." Daniel said unconvinced as he stood to leave. Stevenson weakly waved to him as he left, but followed him with his mind. He felt him stop a few meters outside.

"His physical health is improving and his mind seems stable," Dr. Jackson said to someone in the corridor. Stevenson could feel the other mind but couldn't identify the person.

"But?" the other said. Stevenson heard the voice through Jackson's ears and knew it was familiar…Landry. It was General Landry checking up on him.

"But, I think he's holding back." Jackson guessed.

"Holding back what?" Landry asked.

"I don't know, I'm still impressed by the fact that he's survived this long. When Merlin upgraded me he had to install a failsafe in order to prevent an overload that would eventually kill me. I have no idea how his body is going to be able to stabilize the changes that are happening to him, but he seems confident that he'll make it through." Daniel admitted.

"Oh he does, does he, it might turn out better for him if he doesn't." Landry said.

"Meaning what?" Daniel asked.

"The I.O.A." Landry said simply.

"Oh, not again." Daniel said exasperated.

"I'm afraid so. And there's the little fact that he disobeyed standing orders, which is what created this mess in the first place." Landry explained.

Stevenson released his tenuous mental link. His new abilities were intermittent and unreliable, but he'd been able to hear enough. He knew he was going to have to escape Atlantis…but he wasn't ready yet. He was too weak and continuing to black out. A few more days and he might be able to risk it. He'd only get one chance before they realized what he was capable of and implemented additional security measures.

"_Patience_." he reminded himself.

Sheppard left the hearing demoralized and disillusioned. Good men, men he had respected and trusted in the past had, one by one, sided against him and his actions and fell in line with the I.O.A.'s assertion that what happened in Pegasus didn't matter to Earth and that he had had no right to interfere.

General O'Neill had spoken up on his behalf, suggesting that he be given some leniency since his plans were to fight the Wraith on behalf of Earth. But the I.O.A. wouldn't hear any of it. They felt that the Pegasus galaxy would be better off without Earths interference.

The I.O.A. hadn't bought it and had thoroughly raked Sheppard over the coals. He had argued with them for over four hours but in the end they were going to get what they wanted regardless of the truth. He would be moved onto court martial and probably would live out the rest of his life in a prison cell.

Sheppard was returned to his cell and dropped unceremoniously to the ground. He pulled his back up against the bed frame and cradled his head in his hands. He was screwed and he knew it. Home World Command and his country were going to sacrifice him and the Pegasus galaxy to the corrupt whims of the I.O.A. for whatever deluded or twisted reasons they had.

Sheppard had dodged the bureaucratic bullet many times before, but not this time. He wasn't about to give up, but with his options being what they were, his thoughts were sliding more towards jail-break rather than the defence at his upcoming court martial.

"How are you feeling, son?" O'Neill asked Stevenson. The Captain blinked his eyes open.

"_Headache_." Stevenson complained.

"Don't bother talking, Stevenson, I don't speak Ancient anymore. And I don't feel like dragging Daniel in here, so just listen." O'Neill said with a dismissive wave of his hand.

Stevenson nodded.

"I've deactivated the cameras so this will be a private conversation between the two of us." O'Neill said ominously, which drew a raised eyebrow from Stevenson.

"You're in hot water with the I.O.A., and I'm not sure if we'll be able to protect you. They look at you as a combination guinea pig/data file more valuable than…well, than anything they've come across to date, and in my opinion they're not going to give you up." O'Neill explained.

"I need to know if your head is as scrambled as mine was, or if you have control of the knowledge in your mind." O'Neill said looking up at the observation room to make sure no one was there.

Stevenson raised his hands and smirked quizzically as if saying 'why.'

"If I can feed the I.O.A. some Intel on my terms I can move you out of their reach to one of our more discrete off world bases and dig my political heels in. So long as the information is flowing back to us I think I can protect you." O'Neill offered.

Stevenson shook his head 'no.'

"You don't have control?" O'Neill asked, disappointed but not really surprised. It had been a long shot idea from the beginning ten minutes ago in the commissary.

Stevenson shook his head 'yes.'

"Yes you agree with the 'no' or yes you can?" O'Neill asked confused. Stevenson gritted his teeth then made a snap decision to trust O'Neill. He motioned for him to come closer. O'Neill moved his chair up next to the head of his bed and leaned forward.

"What?" O'Neill asked.

Stevenson reached out and touched O'Neill gently on the right temple. Stevenson's eyes glassed over and a host of images flooded into O'Neill's mind…and suddenly he understood.

Stevenson released the mental link and O'Neill sat up straight.

"Take Sheppard with you. He's in a holding cell down the hall. You've got two more days before he's taken away for court martial. Will that be long enough or do I need to buy you some more time?" Jack asked.

Stevenson gave him a 'thumbs up.'

"Alright, most of the senior staff will be leaving Atlantis tomorrow night for a banquette with the President. That means minimal security and only essential personnel will be here. Can you do it then?" O'Neill had just offered the perfect window of opportunity to Stevenson.

Stevenson shook his head 'yes'.

O'Neill nodded and quickly left the room. He reactivated the security cameras and other recording devices then headed back to the commissary for an extra dessert. He found himself in a much better mood than before, with a hankering for banana pudding.


	6. Chapter 6

Chapter 6

Sheppard was lying helplessly on his small cot behind the cell's bars when he heard a commotion outside

"Hey, what's going on?" he asked into the empty air. Seemingly in response, the huge thick doors of the cell room opened.

"What the hell?" Sheppard muttered.

Stevenson walked into the room wearing an oversized uniform and lifted a hand toward Sheppard's cell. The front panel/door slid open. Stevenson beckoned Sheppard forward with a simple hand motion.

"Okay." Sheppard said slowly, not knowing what was going on but glad for the chance to get out of his cell none the less. They exited the prison room and Stevenson pointed to the unconscious guard, then tugged on his own uniform.

"Right." Sheppard said, looking down at the orange jumpsuit that he was wearing. He knelt down next to the guard and proceeded to swap clothes with him. After he was finished he joined Stevenson at the door that led out into one of the main corridors in Atlantis.

"What next?" Sheppard asked. The man muttered something in a language John couldn't understand, then, seeming to realize that fact, he drew a circle in the air then pointed through it.

"Stargate?" Sheppard raised an eyebrow.

Stevenson nodded.

"After you and your magic hand." Sheppard pointed out the door.

They moved quickly through the halls, with Stevenson telekinetically knocking aside a few personnel as needed. They passed by an armoury and ducked inside briefly, grabbing some essential gear. Forty seconds later they were back in the hallway headed for the control room when the cities alert siren went off.

"Let's move it." Sheppard urged, staying one step behind Stevenson.

A pair of armed guards stepped around the corner in front of them, ordering them to stand down. A split second later the guards were lifted into the air and clunked hard into the ceiling. Their weapons dropped to the ground a moment before their unconscious bodies did.

One of the Zats lying on the floor suddenly leapt through the air and into Stevenson's hand. He tossed it back over his shoulder to Sheppard, who awkwardly caught it in mid-air.

When they reached the lower level of the control room, only two guards were walking around the gate area. Stevenson repeated his lifting trick and the guards were thrown into the wall and knocked unconscious. He was expending a lot of his limited amount of energy…and he knew he had to get through the gate before he passed out again.

"How are we going to dial from down here?" Sheppard asked the tech in the control room looked down at the two men now standing in front of the Stargate.

"Colonel Sheppard, Captain Stevenson, what are you doing?" asked the technician. Sheppard shot her with his Zat and turned back to look at Stevenson.

"Please tell me you have a plan for getting out of here?" Sheppard asked the paling man.

Stevenson visibly gathered himself and set his jaw before stepping over to the side of the Stargate. He reached out and touched it, then closed his eyes. For a moment nothing happened. Then all of a sudden the computer readouts in the control room began showing erroneous feedback.

The event horizon of the wormhole appeared, but without the customary kawoosh beforehand. Stevenson, looking exhausted, walked around and pulled Sheppard forward by the elbow.

He took the hint and followed him through the gate, but not before he paused and looked around at the control room. He'd miss the city for sure. _

Both men emerged into a clearing outside a wide, dark forest. Sheppard stopped just beyond the gate and looked around, trying to get a feel for where they were.

Stevenson, however, immediately went for the DHD. He touched the centre bubble and closed his eyes. The gate shut down a few seconds later and he immediately started to dial another address.

"Smart, they won't be able to follow us if we dial out again." Sheppard said appreciatively.

Stevenson nodded as the kawoosh from the newly formed wormhole jutted out into the blue, sunny sky.

"Come." Stevenson said awkwardly, as if he'd never spoken the word before.

"So you can talk?" Sheppard asked as they stepped into the gate.

They emerged into a desert world with no one and nothing in site. Sheppard thought it looked a little familiar but he couldn't quite place the address.

"What now?" John asked, glad to be free again, but still unsure as to what was going on.

Stevenson pointed at the gate and started dialling another address.

"Again? They shouldn't be able to trace us this far." Sheppard asked.

Stevenson didn't answer. Instead he slowly input seven symbols, then he touched an eighth.

"DHD's can't dial another galaxy, They don't have enough power. Wish they could, then I could get back to Pegasus. But then what would I do, probably get Ronan and Teyla to help build an army." Sheppard said looking around at the surrounding trees.

In response to his assertion the DHD began to light up randomly, as if it were having a motherboard meltdown. Stevenson input select symbols in response to the flashing lights for nearly a minute. Then all the symbols illuminated simultaneously and steadily. He reached up and pressed the centre bubble and activated the gate.

"What the hell?" Sheppard asked.

Stevenson motioned him forward and led him through the gate.

Sheppard's jaw dropped when they emerged on the other side. They were inside a massive facility, obviously of Ancient design, but the most awe inspiring sight was the presence of four other gates sitting side by side with their own. Sheppard stepped out and looked back up at the gate they had come through.

"Holy crap…they're yellow." he said, referring to the chevron lights as Stevenson walked off into the distance.

"Hey, wait up!" he yelled as he looked back at the other gates. One had normal red crystals, while the others had blue, green, and orange chevrons.

Sheppard caught up with him just before he entered an alcove in the near wall that lead to an ascending staircase. He followed Stevenson up and through a latticework of hallways until they stopped before a thick, sealed door.

Stevenson waved a hand over a nearby panel and the 10cm-thick door slid into the wall. Sheppard followed him in and found himself in familiar surroundings. There were Ancient-style control panels, similar to those in Atlantis's gate room, ringing a centre platform with a single podium on its perimeter.

Stevenson walked up to the podium and a holographic map materialized above the platform…identical in every way to its counterpart in Atlantis where he'd first seen a diagram of the Pegasus galaxy.

Sheppard frowned. The map didn't show the Pegasus galaxy, obviously, but it wasn't showing the Milky Way or any other galaxy either. He walked up alongside Stevenson's shoulder as he worked the controls, and with a closer look the significance of what he was seeing finally dawned on him.

"It's a map of the Ancients' galaxies." he said, half looking at Stevenson, but unwilling to take his eyes completely off the map. Out of the corner of his eye he saw the man nod in agreement.

"What is that, two, four, six…twenty two galaxies? That's insane! Where are we?" Sheppard counted.

Stevenson highlighted one of the central galaxies with a white hue.

"And where's Pegasus?" John asked looking at the map. Extra, colourless galaxies materialized around and within the cluster. One of these suddenly highlighted.

"What's that mean? Why isn't it part of the group?" Sheppard asked.

"New." Stevenson finally uttered, visibly forcing the words out.

"New? That's right, Rodney said the Ancients built the Pegasus gates after they left Earth. I guess that puts the count at twenty three." Sheppard asked.

Stevenson shook his head and pressed another button.

All the little dots within the galaxies suddenly connected to each other in a mass of millions of tiny lines that blurred together into a reddish hue…except Pegasus, where there weren't even any dots, just a swirling mass of white.

"Not on the map, huh? Is that why we can't dial out of Pegasus without the Atlantis gate crystal?" Sheppard speculated as another thought struck him.

Stevenson rubbed his forehead and nodded. Apparently he was still feeling the fatigue from their escape.

"Don't supposed you can update the map?" Sheppard said offhand.

Stevenson looked at him worried, then slowly nodded his head up and down, quickly followed by left to right.

"You can but you can't?" Sheppard tried to translate.

Stevenson pointed at the map and input a new command. For a long minute nothing happened, then all of a sudden a dozen or so dots appeared in Pegasus. Then a few more appeared, and more, and more until the entire galaxy was full of new stargate locations.

"Does that mean we can dial Pegasus from here?"

Stevenson pointed at the map again…more specifically at the lines interconnecting gates within and between galaxies. None travelled to Pegasus.

"Not hooked up, huh? You can fix that." Sheppard guessed.

The Captain reached a hand up to Sheppard's chest and pushed his palm flat against it in a feeding motion.

"Don't want to let the Wraith out, I get it. Any way we can still get there? Unless you have somewhere else for us to go?" Sheppard asked.

Stevenson held up a finger, giving Sheppard the 'wait' signal. Suddenly the map zoomed in on the Milky Way galaxy alone, and for the first time he could see that the lines connecting the dots were different colours.

He glanced out the window at the different coloured Stargates on the platform below them and raised a curious eyebrow.

"Where are we?" John asked.

Stevenson highlight and zoomed in on one small dot near the galactic core. Sheppard noticed that lines of all six colours intersected it. He frowned. There had only been five gates, and none of them purple.

"Where's the purple gate?" He asked Stevenson while pointing at the mass of thin coloured lines emanating from their location to what looked like every other stargate in existence. It was hard to differentiate them all, but the colours stood out.

Stevenson pulled up a holographic diagram of them in the control room and zoomed outward through the massive complex.

"We're in space?" Sheppard realized as the diagram resolved itself into a space station with another gate floating outside.

Stevenson nodded 'yes' to his question and highlighted the gate.

"Wait a minute, how big is this station?"

Stevenson brought up a second diagram of an Atlantis-style city for comparison, which overshadowed the complex at approximately twice its size.

"If I'm reading this right, then that gate, is a super gate!" Sheppard said, pointing to the one in space.


	7. Chapter 7

Chapter 7

Stevenson nodded and highlighted all the purple dots within the galaxy. Sheppard saw a hundred or so locations strategically spread throughout various sectors. A connection clicked in Johns mind.

"That's why the Ancient warships didn't have fast hyperdrives. They didn't need to go very far to get to the sector gate. Probably faster to get across the galaxy this way than to travel all the way using hyperdrive. So where's Earth?"

The purple dots faded back to normal and another dot further out from the galactic centre brightened and enlarged. Only red lines intersected it.

"Did all that stuff you did on the DHD have anything to do with these coloured lines and the different colour Stargates?" Sheppard hazarded a guess.

Stevenson nodded. The Colonel's pulse spiked. He had a feeling he was onto something big.

"Are the gates different from each other?" John asked

He nodded again.

"Twenty questions then…do colours only connect to similar colours?" John continued to dig for information.

Again, a 'yes.'

"We came through a red and exited from a yellow, right?" John questioned.

Stevenson nodded and pulled up a diagram of two gates and a DHD that superimposed over the galaxy map. Both gates glowed red and a red line connected them. They disappeared and re-emerged as a red and a green without a connection.

"Ok, different colours don't connect. I get that. So why did we come out a yellow when there was a red a few steps away?" John asked.

The DHD suddenly showed seven symbols highlight. Stevenson tapped a button and an 8th illuminated. When it did the red gate changed colours to green and a connection formed between the two gates.

"Damn, I wish Rodney were here. Ok, so you can change the gate's colour with the DHD?" John guessed and looked to Stevenson for a confirmation.

Stevenson hesitated, rolled his eyes in helplessness, then reluctantly nodded 'yes.'

"What was that look for?" John asked defensively.

Stevenson pointed at the gates outside, then did an amicable job of forming the shape of the gate crystals with his fingers.

"The gates…colours?" Sheppard guessed.

He nodded, then pointed back to the faint dots in the galaxy map.

"I'm sorry, I don't get it." John admitted.

Stevenson blew out a frustrated breath and reached a hand up to Sheppard's temple. A moment later the Colonel suddenly understood and the Captain looked even more exhausted than before.

"Neat trick, the crystals don't actually change colours, but the gates act like they're a different colour." Sheppard said, a bit impressed and creped out at the same time.

Stevenson nodded, relieved.

"So why didn't we come in through the red gate?" John asked still a little confused.

Stevenson pointed at his chest and shook his head 'no.' He pointed away from himself and shook his head 'yes.' Sheppard glanced back at the gates for a second before catching on.

"You can dial out, but not in? Some type of security precaution?" Sheppard guessed and Stevenson confirmed with a tired nod.

"So we got here by switching colours, which you managed with the extra symbol on the DHD. I thought that was for dialling another galaxy." John said.

Stevenson again nodded.

"How can it do both?" Sheppard frowned.

He held up nine fingers in response.

"Ninth chevron? It moves us between different colour gates?" Sheppard said as his jaw dropped.

Ryan shook his head 'yes'.

"But you only input eight chevrons?" John remembered.

Stevenson used the DHD diagram and input the standard six symbols, then the point of origin, then the activation bubble in the centre. A line connected the two Stargates, both of which had been reset to red before he began. He held up a finger to forestall another question and input the standard six symbols again, then a seventh, then the point of origin. The gates connected and a galaxy to galaxy line appeared.

"Intergalactic." Sheppard noted. John watched as two gates switched to one red, one green. Stevenson re-input six commands, the point of origin, then another symbol before hitting the activation bubble.

The two gates connected when the green gate turned red. Stevenson pointed to the point of origin icon in the string of eight symbols hovering just below the DHD.

"It comes after the point of origin. So that's why it doesn't dial intergalactic." Sheppard said, catching on.

Stevenson reset the diagram one more time with one red gate and one green gate. He input six icons, then belatedly a seventh, then the point of origin, then the ninth chevron before finally the activation bubble. The green gate turned red again, but this time the intergalactic connection showed up again.

"Eight for in-galaxy gate-jump, nine for intergalactic gate-jump?" Sheppard asked, feeling like a Stargate rookie getting his orientation lesson. And to think, the SGC and the IOA thought they had a complete list of every stargate within the Milky Way galaxy. The Ancients had far better security than he'd ever given them credit for.

Stevenson nodded curtly, apparently satisfied, and turned back to the map. He got rid of the diagram and input some new commands. Another long pause ensued while the computer worked on something.

"What was with all the flashing symbols when you dialled?" John asked.

Stevenson held up his forearm and started tapping on his wrist, pretending he had a GDO.

"Some kind of access code?" Sheppard said as he raised an eyebrow.

Stevenson nodded as a few of the dots on the map began to disappear.

"Dead gates?" Sheppard guessed.

He nodded regretfully. Once the system completed the update, Stevenson scrolled through a list of planets and found the one he wanted. It was listed as having a green stargate only, and suddenly the green gate outside the window flashed to life, but without the corresponding kawoosh. The event horizon just popped into place.

"We moving on?" Sheppard asked, adjusting the pack on his shoulders.

Stevenson held up the wait finger again.

A picture materialized over the galaxy map, revealing another large chamber with ancient-looking tech. This one had numerous struts extending from floor to ceiling with what looked like workstations spread around their bases.

"Are we seeing that through the gate?" John asked.

Stevenson nodded.

"Did you send a probe through?" John said as he watched the screen.

Stevenson shook his head 'no' this time. He made the stargate circle symbol with his finger.

"The stargate? Wait a minute, are you saying the Stargates have a camera in them?" Sheppard asked in shock.

Stevenson turned to look at him and nodded an ironic 'yes.'

"Why the hell didn't Rodney find that? Ah…of all the times we needed Intel about what was on the other side of the gate we had the perfect tool right under our nose!" John complained. Stevenson motioned to Sheppard to come with him as he headed for the door.

"Guess we're going." John shrugged.

They wound their way back through the maze of hallways and down the staircase. When they got to the green stargate it was still open and Stevenson walked through without preamble. Sheppard followed close behind, glancing up at the green crystals just before he passed through.

They both emerged on the other side into what Sheppard immediately guessed to be some factory. He didn't have any hard evidence to back that theory up, but the congestion of equipment and lack of windows gave it that feel to him.

Stevenson quickly found the control panel he wanted and suddenly the entire facility hummed to life with a restored power flow. He brought up a display screen and a list of data. He highlighted several sections and hit an overly large button on the control panel in front of him. Sheppard glanced over his shoulder as the machinery started to activate, doing what he couldn't imagine.

"What is this place?" Sheppard asked.

Stevenson motioned for him to follow, and together they worked their way through the now active facility into a storage depot on the opposite side of the complex. Inside Sheppard saw small, empty racks lining the walls and partitions.

"What are these for?" Sheppard asked. Stevenson reached into the one and only occupied alcove in the depot and pulled out a ZPM.

"No way!" Sheppard said in utter shock.

Stevenson held up two fingers.

"Two? Where's the other one?" John asked.

Stevenson pointed out into the centre of the facility. Sheppard glanced out the door, then back to the numerous empty racks.

"Does this place make the ZPMs?" John asked.

Stevenson smiled…and nodded 'yes.'

"Now that's what I'm talking about." Sheppard said as he fist-pumped the air. The Captain smiled and motioned for him to follow. He led him back to the gate and reactivated it. Sheppard glanced back at the active machinery.

"How long is it going to take to make another?" John asked.

Stevenson made a looping motion with his outstretched finger.

"A while," Sheppard translated as he followed Stevenson back through the gate.

When they got back to the 'gate centre', as Sheppard thought of it, he noticed that they'd come back through the yellow gate again, not the green gate that they'd left through. He guessed yellow had a higher security rating than green, and followed the Captain back across the open platform to the wall alcove and the stairway to the control room.

Instead of going back there Stevenson led him further into the facility and into what looked like personal quarters. They both pulled some rations out of the packs they'd grabbed from the Atlantis armoury and stretched out on the low beds. The cushioning had long since deteriorated, but the solid slab that was left proved adequately relaxing.

Stevenson finished his rations and laid down in a meditative pose. He remained motionless for the following six hours, in which Sheppard sat with his back against the wall, relishing his regained freedom and the awesomeness of where he currently was.

After soaking it all in he finally managed to fall asleep.


	8. Chapter 8

Chapter 8

When Sheppard woke up ten hours later he found Stevenson's bed empty.

"Now where did he go?" John whined as he stood up from the low bed and grabbed at his soar back. Sleeping on a stone slab was as bad as it sounded. After stretching a bit he ventured outside the door and tried to get some sense of where Stevenson had gone.

With neither a sight nor a sound to go by, he decided to backtrack to the command centre and found Stevenson once again at the holographic controls.

"There you are don't go wandering off like that." John said pointing a finger as if he was talking to a child.

Stevenson glanced over his shoulder and said something in Ancient.

"Apology accepted, What have you been up to?" He asked as he glanced out over the multi-galaxy map again. There seemed to be fewer dots amongst the other galaxies this time but a number of interconnecting lines within Pegasus had been added, but without any extragalactic lines. There were, however, a few dots in between galaxies that he guessed were the remains of the gate bridge.

"What happened here? And what is that?" Sheppard asked as he noticed another new galaxy far outside the Ancients' territory. It was connected to the Milky Way by a solitary gray line.

Stevenson made the symbol for stargate with his finger.

"Stargate." Sheppard said.

Stevenson formed an 'O' with his fingers and expanded it outward.

"Bigger you mean super gate?" John guessed.

He nodded and pointed at the two ends of the gray line.

"That's the Ori galaxy?" Sheppard asked.

Stevenson gave him a thumbs up.

"You can tap into their network from here?" Sheppard questioned.

The Captain held his hand up and wiggled it.

"Kind of partially?" Sheppard guessed.

Stevenson held his fingers up and pointed at his eyes and then at the super gate connection.

"See you can see it? You can detect it?" John enquired.

Another thumbs up.

"But you can't control it?" Sheppard waited for confirmation.

Stevenson shook his head 'no.'

"What about Pegasus, can you control their gates?" Sheppard asked.

Thumbs up again.

"Can you get us back there?" John questioned.

He nodded and held up three fingers.

"Three what?" Sheppard asked.

Stevenson held his hands about a foot apart, one above the other.

"ZPM? Three ZPMs? For what?" Sheppard questioned.

Steven held up his index finger and tapped his nose.

"What are we going to do until then?" John said expressing his concern.

Stevenson shook his head 'no' and reached out to Sheppard's temple again. A moment later he released him, his eyes wide with surprise.

"That could work." were all the words Sheppard could manage in total shock.

* * *

><p>The cloaked city of Atlantis sat in San Francisco bay, a few thousand meters away from the Golden Gate bridge. Since Atlantis's return to Earth, two of her ZPMs had been taken away from her and given difference assignments. With one of the modules more than capable of powering the cloak for a few years, there was no rush to find a suitable place to hide the city. The I.O.A. were looking at relocating the city to Antarctica, but it was proving difficult.<p>

Richard Woolsey had just returned to the city, like most of the other senior staff, after a banquet with the President and I.O.A. officials. He returned to absolute chaos. Colonel Sheppard and Captain Stevenson had escaped while most of the city's personnel were at the banquet. This would surely infuriate the I.O.A. and cause him a great amount of stress.

"Incoming wormhole." Someone shouted from behind Woolsey.

"Who could that be? We don't have any teams off world." Atlantis's commander asked.

"We're receiving no IDC, sir." Chuck, the technician informed.

"Keep the shield up." Woolsey ordered just before the shield dropped, exposing the incoming wormhole.

"I said keep the shield up!" He yelled, glaring at the tech sitting at the dialling station.

"It wasn't me, sir. My controls are being overridden. I can't raise it again!" Chuck said panicking.

"Security to the gate room! Find out where that override is coming from and some way to get around it." Woolsey yelled in panic as he started to backtrack from the open gate.

"What's going on?" Major Lorne asked as he ran into the gate room.

"We don't know and we can't raise the shield." Woolsey explained.

"John!" He suddenly exclaimed as Sheppard and Stevenson walked through the gate.

"What the hell? Why did you come back?" Woolsey said as he darted back down the stairs.

"Sheppard!" Ronan yelled excitedly as he entered the gate room a few seconds behind Lorne.

"Hey buddy, good to see you." John smiled.

"Arrest the Colonel!" Woolsey insisted as they walked up face to face in front of the gate.

Before Sheppard could smart off, Stevenson reached his hand out and the control pillar shot up from the floor. He placed his hand on it and suddenly the lockdown alarm sounded.

"What the hell is going on? Security!" Woolsey demanded. Four SF's stepped forward and raised their guns on the pair while another three started to come down the staircase.

Stevenson raised a hand and ripped the guns away from the nearest two. A split second later Sheppard pulled out his Zat and shot one of the others. Ronan got the fourth with a quick draw before the man could fire at Sheppard.

The three coming down the staircase quickly took fire from both Sheppard and Ronan while Stevenson relieved another of his weapon. Within seconds the gate room was back in their hands.

"Thanks buddy." Sheppard said to Ronan as he trained his Zat on Woolsey.

Stevenson, meanwhile, darted up the stairs and ran to the city control board and raised the city's shields.

"Are you insane? What are you doing?" Woolsey asked almost simultaneously.

"He stuck his head in an Ancient microwave and got superpowers. I meanwhile am just along for the ride. So with his powers and my good looks, we're stealing the city." Sheppard said sarcastically as Woolsey's radio buzzed with static.

"Daedalus to Atlantis, why did you raise shields? Do you realise the whole of San Francisco can see you?" Caldwell asked, quite miffed.

"Ronan, keep them under guard." Sheppard ordered as he bounded up the staircase.

"Move." he told the tech at the dialling station.

The man slid out of his seat while Sheppard dialled Earth.

"What's going on?" Chuck asked, very concerned.

"We're not going to abandon the Pegasus Galaxy." he answered bluntly.

"And by us you mean?" Chuck asked.

"By us I mean me and my new best friend." John indicated to Ryan.

"And he is?" Amelia asked, frowning.

"Captain Stevenson, he can't talk but he can still hear us just fine." Sheppard answered.

"Wait a minute, the two of you are planning to take over Atlantis on your own?" Ronan asked.

Sheppard glanced over at Stevenson, who gave him a nod of confirmation as he continued to work the controls.

"Actually, we already have." John smirked.

"Who'd you get to lower the shield for you? McKay?" Woolsey asked snobbishly.

"Nope, he did." he said, pointing to Stevenson.

"How?" Woolsey asked incredulously.

"None of your concern." Sheppard said as he nodded at Ronan. Ronan recognised the hint and shot Woolsey with his weapon.

"I hope that was set to stun. Lock them in their quatres." John nodded. Ronan just smiled as Sheppard snatched the radio from Woolsey's shoulder, cutting off Caldwell's continued questions with a quick flick of the switch.

"Are you sure you know what you're doing?" Ronan asked.

"Too late too turn back now if I wasn't." Sheppard said sarcastically.

"Yes, I'm sure." John replied.

He nodded that that was good enough for him and started to drag one of the unconscious guards toward the transporter.

"How are we doing?" John asked Stevenson.

The Captain pointed to the comm. button.

"Alright, here goes nothing." he said, placing his hand on the panel and activating the city-wide intercom.

"Everybody listen up. This is Colonel John Sheppard, acting commander of Atlantis. I've taken control of the city and initiated a comprehensive lockdown, so just sit tight for a while, you're not going anywhere for a couple of hours." John began.

"In my opinion both the I.O.A. and Stargate Command have crossed the line when they decided to abandon the Pegasus galaxy to the fate of being Wraith food. I would like to think Earth is better than that, but recent events have shown me otherwise." Sheppard continued.

"I, however, am not going to abandon Pegasus. I've already been declared an enemy of Earth, if not I will be soon, so I don't have the luxury of staying but you do. So you have a choice to make." John continued.

"Anyone that wishes to help us fight the Wraith will be welcome to, but it will mean never returning home to Earth, as well as imprisonment if we are ever captured." John explained.

"I know this is a lot to throw at you all at once, but you're going to have some time to think it over as long as the lockdown is in effect, so think hard. You won't get a chance to change your mind either way. If you choose to go back I won't hold it against you personally. I'll understand if you can't bring yourself to turn against Earth. For me, with a court martial waiting for me, it's an easy choice. For you I know it won't be." John admitted.

"Talk amongst yourselves, think it through. Contact the gate room over the comm. when you finally decide, or wait for us to come around room by room. Figure a couple of hours at least. Sheppard out." Sheppard finished. Ronan joined Sheppard in the control room after locking the small group in a nearby storage room.

"I assume you are with us?" John asked.

"I get to kill Wraith? I'm in." Ronan gruntted.

"Just checking, What about the rest of you. Anyone want to turn renegade?" Sheppard added.

The half dozen people in the control room exchanged glances and bashfully shook their heads 'no.'

"Ok." Sheppard said, expecting as much.

"Take them back to their quatres." John ordered.

"What about you Lieutenant?" John asked the only conscious Air Force officer in the control room.

"Devonshire, sir, I'm with you." Devonshire nodded.

"Good, help Ronan escort this batch back to their quatres." Sheppard said.

"Yes sir." Devonshire nodded.

"Stevenson, you going to start your 'screenings'?" John asked and was just nodded at as the man headed for the transporter.


	9. Chapter 9

Chapter 9

Five and a half hours later the wormhole to the Pegasus Galaxy was opened. Most Atlantis personnel had been interviewed without incident, but a few SF's had to be physically subdued. The last group of those willing to fight the Wraith walked through the gate, leaving Sheppard, Ronan and Rodney standing in front of the portal back to Pegasus.

"I'm sorry." McKay said for the fiftieth time.

"I understand, Rodney, you've got to do what you've got to do." Sheppard said, placing a hand on his shoulder.

"It's not that I don't want to go with you, but I can't live with the thought of never seeing Jennifer or my sister again. But then again I don't want to abandon you guys either despite the fact that you have zero chance of pulling this off, and with me staying you'd at least have a small chance of staying alive " Rodney complained.

"Rodney, it's ok." Sheppard interrupted.

McKay wanted to say something more, but couldn't find the words. He stepped forward and hugged Sheppard, who returned the gesture without hesitation or complaint.

Ronan starred down McKay when he approached him with intent to hug, then softened and dragged McKay over, lifting him up off the ground in a giant bear-hug.

"Take care." Ronan whispered.

McKay looked back at all of them, trying to find the right words.

"Good luck." He said simply, as Ronan and Sheppard stepped slowly and reluctantly through the gate.

McKay wiped a tear from his eye and walked back up to the control platform. He pressed one of the comm. buttons.

"Colonel Cladwell, Sheppard just left, what should I do?" Rodney asked the air. Rodney knew this wasn't good.

Most likely people all over San Fransico city were in shock at the sight of a massive, shielded city appearing in the bay. Recordings and pictures would no doubt be uploaded to the internet within minuates.

* * *

><p>Off in Pegasus, Sheppard and Ronan exited the Stargate to find themselves in the middle of a grassy medow surrounded by large trees. The moonlight wasn't bright enough to show every individual face, but it was bright enough. Stevenson heard Sheppard's voice announcing his arrival and looked up from the DHD.<p>

The gate dialed as Stevenson pressed the symbols he wanted. Sheppard and Ronan recognised the gate address immediatly. Stevenson had the three ZPMs in a pack strapped to his back. The group of thiry or so 'defectors' that had decided to help fight the Wraith, were all stood behind Stevenson and the DHD. Most, if not all, were silently wondering if they'd made the right choice as they watched the gate activate.

People all around the gate watched as Stevenson walked through. Sheppard nodded and the group began to follow him through. John and Ronan were the last two to go through the gate. Sheppard and Ronan covered their eyes from the midday sun shinning in their eyes, as they exited the stargate.

Rubbing their eyes, the whole group looked at their surroundings. Trees and grass were the first two features that they noticed first. As their eyes focused and adapted to the sudden change in light, everyone could see the copy of Atlantis's Control Tower standing up above the treeline.

Sheppard walked past Stevenson and looked at the tower.

"So, Stevenson, is this our new home?" John asked. But he was no where to be seen.

"He just ran off." Devonshire said, stunned.

"Super speed is so cool." John smiled.

* * *

><p>Stevenson was still on the move, and had been ever since he'd entered what was left of the crumbling city. Currently he was in the holo-room going through the updates to the Ancient database that had occurred since the construction of the Repository of Knowledge. He knew far more about the Ancients than any living person, but the Pegasus Ancients, or Lanteans, were a complete mystery to him. Hence he had a lot of catching up to do before he started to tackle the challenges ahead of him.<p>

"Are you in pain?" A voice from behind him spoke in Ancient.

"Yes, but I'm managing." Stevenson said, turning around to face the ascended Ancient.

"I apologize for the discomfort that you must endure, but I could find no other way. Your body is in a constant state of flux, and will remain so for quite some time. Until your advancement reaches a level where you can defend yourself from ascended beings. Once you reach that point you will have a choice: let the changes plateau or push on further." The man explained.

"And if I continue on?" Stevenson asked.

"We don't know. No one has ever been allowed to develop that far." The image of the Ancient man shrugged.

"Tell me about the others. You must have learned more over the past few million years?" Stevenson asked. The Ancient's expression tightened.

"Yes. They're not all ascended beings, as we first believed. The core of the Ascended Empire is made up of a nameless race of energy-based life forms. They are the ones who have forced the assimilation of ascended beings into the Empire, and they are the origin of the non-interference and limited development edicts. They have a distaste for corporeals and, I think, they also don't want us interacting with our previous species." He explained. This caused Stevenson to raise an eyebrow.

"How many other species are we talking about?" Ryan asked.

"Hundreds, if not thousands. Humans are one of the newer additions to the group. We're discouraged from information gathering, I think the Originals, that's what we refer to them as, like to keep us in the dark as much as possible. We have surmised that the Empire's domain extends through several hundred galaxies but, ironic enough, seems to end somewhere between Avalona and Destra." The ascended man explained to Ryan.

"Really, the Ori weren't part of the Empire?" Stevenson remarked.

"Oddly enough no, though they were closely monitored to determine if they would ever become a threat to the Empire. They knew that if they ventured into the Originals' domain they had to operate under their rules, but as long as they stayed outside of their territory and posed no threat to them, they were essentially free to do as they pleased." The man continued.

"Interesting. Why didn't you and the others leave their domain?" Ryan asked, intrigued.

"Once part of the Empire, forever are you bound to it. A few of us tried to leave and were tracked down by the others. Some returned...those who didn't were killed." The Ancient sighed.

"Are you in danger talking to me?" Ryan asked, concerned. To which the man shook his head.

"The Universe is a big place, the Originals and their followers can't watch over everything. Some of the Alterra have, regrettably, assimilated into the Empire and assist them in watching us. I've been given a short window of time to meet with you while a few loyal Alterra distract them. It is doubtful I'll be able to consult with you again without drawing you unwanted attention." The Ancient warned.

"I understand. What else do I need to know?" Stevenson nodded.

"My name is Lyran. I'm the one who developed and added the secondary programming to the Repositories with the help of a few non-ascended Alterra before they finally died of the plague. I wasn't allowed to help them ascend and was forced to watch them die helplessly. To make matters worse, I've also discovered that it was the Originals who created the plague. They deemed us too dangerous and decreed that we could not be allowed to advance any further. They are also the ones responsible for killing the Asgard by tampering with their DNA and causing their gradual deterioration as well as their inability to ascend." Lyran explained.

Stevenson's hands balled into fists. Blood dripped from where his fingernails were cutting into his skin. While he might not have been blood kin to the Ancients, the changes the Repository had made to his body and mind had essential turned him into one of them and he found himself taking the news of their murder personally.

"Now you understand how far they will go to insure that no corporeal species will ever threaten them. They also have to limit the number of new ascensions for fear of us one day outnumbering them. They tolerated the few of us that ascended, but made sure that no Asgard would, given our former alliance. The Originals and their Empire are not to be trifled with. You must be very careful, and very patient. Once you show your hand we won't get a second chance at this." Lyran warned.

"I plan to stay here and deal with the Wraith while I develop. What of the Furlings?" Stevenson nodded slowly.

Lyran shook his head.

"I would not involve them so soon. They are still in Ryss and Nextor, and have yet to attract the attention of the Empire. Do not involve them until you are in a position to protect them." Lyran explained.

"I'll keep that in mind. At least they're still alive." Stevenson said gratefully.

"Alive, but at risk. They are currently involved in a war of their own against an enemy far more powerful than the Wraith. Don't get involved in their fight until you're ready." Lyran warned.

"What can you tell me of the Wraith? How did they defeat the Lanteans?" Stevenson asked and Lyran glared with contempt.

"The Lantean civilization was too focused on developing to the point of ascension. They lost the war out of pure stupidity. If you use the technology available to you wisely, you should have no trouble defeating them." Lyran said, glancing over his shoulder.

"I must go. Good luck, brother." Lyran said before he faded from view, leaving Stevenson alone in the holo-room. He wiped his bloody palms off on his pants, revealing smooth skin beneath, his cuts had already healed.

He took a moment to gather his thoughts and get his emotions back in check, then he returned to his search through the database. He couldn't afford any missteps with the Wraith out of ignorance. It could jeopardize everything.


	10. Chapter 10

Chapter 10

"Excuse me for saying so, but I find it hard to believe that the few of us that are willing to fight, have any chance of defeating the Wraith." Laura Devonshire interjected from her seat in the royal council chambers that the Lady-Provider, or Mara, was allowing them to use.

It was a simple hall that looked like something out of Lord of the Rings. A large fire, fabric decorations and wooden furnature only reinforced the medeval theme of the room. Sheppard glanced at Stevenson, then back at Devonshire.

"We do have our own Ancient now." John indicated to Stevenson.

"Yes, I noticed, but we've lost all support from Earth. No ships, no weapons, no soldiers and no food." Laura countered.

Stevenson jutted a thumb at his chest.

"I think that means he's got it covered." Ronan speculated. Laura raised an eyebrow.

"How, exactly?" The Ex-Lieutenant asked.

Stevenson opened the case lying in front of him on the table. He pulled out a small vile with gray dust inside.

"Nanites!" Laura exclaimed.

"You mean Replicators? That's an insanely bad idea." Sheppard replied, stunned.

Stevenson shook his head

"Toooollls," He said, not quite getting the pronunciation right.

"Wait a minute? Are you saying we can use those things to build whatever we need?" Ronan said, leaning forward in his seat.

Stevenson nodded.

"Cool, why didn't we think of that earlier?" Ronan asked looking to Sheppard.

"Because Replicators have a habit of not taking orders, I'm hoping these are different somehow?" Sheppard said.

Stevenson nodded emphatically.

"I'm wondering, is this how the Ancients originally built Atlantis?" Laura inquired.

Stevenson rotated his hand side to side in front of him.

"That means 'sort of.'" Sheppard translated.

"Good enough for me, as long as you know what you're doing." John said, glancing at Stevenson.

"Do you mean to involve the humans in the Pegasus galaxy in our fight, or do you intend to build an army of Replicators to fight for us?" Devonshire asked both Sheppard and Stevenson.

"I had expected to bring volunteers here and begin training them. Starting with the Athosians." Sheppard said hesitantly.

Stevenson nodded his approval.

"As for using Replicators, you already know where I stand on that." John added.

"But does he?" Ronan asked.

All eyes fell on Stevenson.

He reluctantly pulled out a data pad that he'd managed to grab from Atlantis before they'd left and meticulously typed in a message. He slid it across the table in disgust at his own inability to communicate, temporary as it may be.

"What did he say?" Laura asked when John didn't immediately say anything.

"Seems he isn't opposed to using the technology, but he doesn't like the way the Lanteans built them to fight their war for them. At the least he intends to build some to use for security in the city." Sheppard said, shaking his head.

"I am not going to agree to that unless you can 100% assure me that what happened the first time isn't going to happen again." John added.

Stevenson motioned for the data pad back. He typed a quick message, and then returned it.

"Lanteans were stupid, they programmed them to be autonomous and aggressive. Ours will be neither." Sheppard read aloud for the others to hear.

"Forgive my bluntness, but if you have the Replicators, what do you need humans for?" Laura asked.

"Good point." Ronan added.

"Much." Stevenson said, almost normally.

Laura raised an eyebrow.

"Like what?" She asked.

Stevenson retrieved the data pad again. This time he slid it to Laura when he was finished.

"He says that machines can only do what they're programmed to do. They can't think for themselves, they have no sense of right and wrong. They are only tools. Nothing more." Laura read it out loud.

Devonshire placed the data pad back on the wooden table, already feeling better about Stevenson.

"I agree and perhaps Teyla can convince the Athosians to help." Laura offered.

"There's an idea." Sheppard said, pleased.

"Ronan, how do you feel about training ourselves an army to fight the Wraith?" John asked.

"About time." The Satedan smiled.

"Alright then." Sheppard said, standing.

"Stevenson, your the only one who can properly repair the city. We'd just get in your way." John half joked, half seriously said.

Stevenson stood, gave him a thumbs up, and then left the room through the guarded door.

"This whole not talking thing is starting to get annoying." Ronan said after he'd left.

"It is a little weird, but he doesn't have a choice. His mind was reprogrammed to speak Ancient the same way General O'Neill's did. I'm just glad he can understand us." Sheppard admitted.

"Perhaps he'll be able to relearn English again, He has managed a few words." Laura suggested.

"It's either that or he gets to carry a blackberry around the rest of his life." Sheppard said sarcastically as they left the briefing room.

* * *

><p>Forty three minutes later, Sheppard ventured into the city to bring Stevenson some food. It took about an hour for John to actually find Stevenson in one of the lower levels of the Control Tower. Now that they'd switched planets and addresses, it was unlikely that Earth would be able to find them again if they were going to look for them at all.<p>

Sheppard wasn't sure what they would do. They had wanted out of Pegasus pretty bad, but now that he'd stolen key personel from them they were sure to be pissed he just didn't know how far they'd go to come after him and the others who'd chosen to go rogue.

And he really didn't like the idea of having to throw down against their own battle cruisers, but he knew that was a distinct possibility.

At least their new location would buy them some time to get organized and re-geared for their self-proclaimed war against the Wraith. Sheppard still had no idea how they were going to fight that war, but Stevenson had been adamant that they could win without assistance from Earth, and after what he'd shown Sheppard in the Milky Way, he was eager to see how this was going to play out.

Sheppard enetered the room and immediatly looked at the clear container Stevenson was carrying.

"That's a lot of nanites, where did u get them from?" Sheppard asked.

Stevenson merely tapped his nose with his index finger while continuing with his work.

"Whatever, so are those the security Replicators?" John asked.

Stevenson shook his head 'no' and stepped over to a control panel where he brought up a map of their current location. It rotated until they could see both the city and several kilometres beneath the surface of the planet. The Captain highlighted several deposits of Naquadah and Neutronium in close proximity to the city.

"Mining." Ryan said, again managing a word in English.

"Cool." Sheppard said as Stevenson stopped the inflow of new nanites. The two canisters disappeared downward into the floor.

"Where are they going?" John asked leaning over to try and locate the canisters.

Stevenson brought up another schematic that showed the canisters being moved down a shaft to the underside of the city. From there they would be released into the soil and work their way down into the bedrock, building micro-conduits as they went that would funnel the raw material back up into the city for the repairs to begin. Stevenson then handed Sheppard a case of vials and a data pad.

"What's this?" He asked. He looked at the screen and found it to be another translation.

Take the canisters and release the contents on the following worlds. They are pre-programmed to activate ten seconds after the seals are broken. Don't open them until you are in position. These nanites will begin gathering other materials we need and will report back to the city via subspace.

Sheppard glanced down at the two dozen addresses listed below the message and was suddenly glad for something to do other than follow Stevenson around.

"Will do." he said as he picked up the case and left Stevenson to his work. He radioed Devonshire and Ronan to have them meet him at the gate.

"What are those?" Ronan asked.

"Our cargo. We're going to make some deliveries." Sheppard told him while signalling the sparse control room staff to dial the gate.

"About time we had a mission, we've been sitting on our butts for too long." Ronan remarked.

"I agree, it's time we got back to work." Laura smiled. Sheppard smiled as the kawoosh retreated back into the event horizon.

"It's good to be back." He said as the three stepped through the gate together.


End file.
